Genetic variation and immunogenic epitope prediction of Vietnamese porcine reproductive and respiratory syndrome virus (PRRSV)

Abstract

Porcine reproductive and respiratory syndrome is a devastating disease that causes heavy losses to the economy and the development of agriculture. In this study, we aimed to assess genetic variation of the ORF5 gene and NSP2 gene from 12 Vietnamese porcine reproductive and respiratory syndrome virus (PRRSV) strains. ORF5 and NSP2 gene were amplified with specific primers. The PCR amplicons were used as templates for sequencing. MEGA 6 program was applied to assess the genetic variation and phylogenetic analysis. The hydrophobicity of GP5 was analyzed by Kyte and Doolittle method. Our results showed that the Vietnamese strains were separated into two clusters, in which five strains BG/12, TG1/12, TG2/12, TG3/12, TG4/12 were grouped in cluster 1 and the left strains were belonged to cluster 2. The N21 glycosylation site (N→S) of GP5 sequence was mutated in five Vietnamese strains from cluster 1. The core sequence of the neutralizing epitopes (including five positions at H25, Q27, I29, Y30 and N31) in GP5 was presented in all Vietnamese strains excepting strain TG1/12. The hydrophobicity plots of GP5 revealed two amino acid positions of BG/12 strain which was different from CH-1a strain and VR2332 strain including in position 85 to 95 and position 100. There were 4 new amino acid substitutions of NSP2 from Vietnamese PRRSV strains at positions A24V, V63A, S198G and N201D. The identity of amino acid sequence between Vietnamese PRRSV strains with Henan-1 strain (92-97%) was higher than VR2332 strain (81- 84%). Two putative epitopes ECVQGCCEHKGLLGSPD and LCQVIEDCCCHQNKTN were highly conserved in Vietnamese PRRSV strains. The phylogenetic analysis of ORF5 and NSP2 sequences of Vietnamese strains and other strains indicated that the Vietnamese strains belong to type II. Keywords: PRRS, ORF5, NSP2, Vietnam